Results for "Correction"

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  • LoRDEC: a hybrid error correction program for long, PacBio reads

    LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and ...

    Tags: Bioinformatics, LoRDEC, Hybrid, Error, Correction, Program, Long, PacBio, Reads, Illumina

    2545 days ago

  • Pollux: platform independent error correction of single and mixed genomes

    Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer err...

    Tags: Pollux, Platform, Independent, Error, Correction, Single, Mixed, Genomes

    2506 days ago

  • Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

    Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make...

    Tags: Oxford, Nanopore, Sequencing, Hybrid, Error, Correction, de novo, Assembly, Eukaryotic, Genome

    2312 days ago

  • Jabba: Hybrid Error Correction for Long Sequencing Reads

    Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph should appear in fasta format with 1 entry per node...

    Tags: Jabba, Hybrid, Error, Correction, Long, Sequencing, Reads

    1945 days ago

  • ECTOOLS: Long Read Correction and other Correction tools

    Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsare at the bottom of this file. Contact: gurtowsk@cshl.edu In short, the correction algorithm takes as input the u...

    Tags: Long, Read, Correction, Correction, tools, ectools

    2275 days ago

  • LRCstats: Long Read Correction Statistics

    LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation sequencing technology, as the name suggests, are lon...

    Tags: LRCstats, Long, Read, Correction, Statistics, pacbio, nanopore

    2275 days ago

  • Pacasus: Correction of palindromes in long reads from PacBio and Nanopore

    Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder: https://github.com/swarris/Pacasus/blob/master/vib2017.pdf. The prepint version ...

    Tags: Pacasus, Correction, palindromes, long, reads, PacBio, Nanopore, ngs

    1964 days ago

  • HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning

    HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments.  HECIL’s core algorithm by introdu...

    Tags: HECIL, Hybrid, Error, Correction, Algorithm, Long, Reads, Iterative, Learning, longreads

    1914 days ago

  • MEC: Contig Misassembly Correction

    MEC, to identify and correct misassemblies in contigs. Firstly, MEC takes fragment coverage as the feature to detect the candidate misassemblies. Then, it can distinguish a large number of false positives from the candidate misassemblies based on the distribution of paired-end reads and the stati...

    Tags: MEC, Contig, Misassembly, Correction, assembly

    1514 days ago

  • proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

    proovread : large-scale high-accuracy PacBio correction through iterative short read consensus outperforms PacBioToCA/LSC in terms of accuracy and contiguity/sensitivity (http://dx.doi.org/10.1093/bioinformatics/btu392) is easy to install/run/configure supports various types of dat HiSeq/...

    Tags: proovread, large-scale, high-accuracy, PacBio, correction, iterative, read, consensus

    2275 days ago